Arndt von Haeseler


Email: arndt.von.haeseler(AT)univie.ac.at
Phone: ++43 +1 / 4277 - 74307

Postal address:
Center for Integrative Bioinformatics Vienna (CIBIV)
Max Perutz Labs
Campus Vienna Biocenter 5 (VBC5)
A-1030 Wien, Austria

Publications:
The full list of publications is available at Google Scholar

Research interests

  • Phylogenetic inference
  • Phylogenomics
  • Neural Networks
  • Sequence evolution
  • Complex patterns of evolution

Education

  • 1994: University of Munich, State doctorate (Habilitation) in Zoology
  • 1988: University of Bielefeld, Ph. D. in Mathematics
  • 1984: Philipps University Marburg, State examination (1. Staatsexamen) for biology, mathematics, education science

Professional Experience

  • since October 2010: Full Professor for Bioinformatics at the Center for Molecular Biology and Department for Computer Sciences (University of Vienna) and at the Department for Medical Biochemistry (Medical University of Vienna), Austria
  • since 2005: Scientific Director of the Center for Integrative Bioinformatics Vienna (CIBIV).
  • Apr 2017 - Mar 2020: Dean of the Center of Molecular Biology at the University of Vienna; Head of the Center for Medical Biochemistry at the Medical University of Vienna; Scientific Director of the Max F. Perutz Laboratories
  • Sept 2005 - Sept 2011: WWTF Science Chair for Bioinformatics and Full Professor at the Medical University Vienna, the University Vienna, University of Veterinary Medicine, Austria
  • 2002 - Aug 2005: Chairman of Computer Sciences, Heinrich Heine University, Düsseldorf, Germany
  • 2001 - Aug 2005: Full Professor (C4) for Bioinformatics, Heinrich Heine University, Düsseldorf, Germany
  • 2001-2004: Group Leader of the Bioinformatics Group at the Neumann Institute for Computing, Research Center Jülich, Germany
  • 1998-2001: Group Leader (C3) of the Theoretical Biology Group, Max Planck Institute for evolutionary Anthropology, Leipzig, Germany
  • 1995-1998: Senior Scientific Lecturer (Hochschulassistent, C2), Biology Dept., Ludwig Maximilians University, Munich, Germany
  • 1991-1995: Scientific Lecturer (Hochschulassistent, C1), Biology Dept., Ludwig Maximilians University, Munich, Germany
  • 1990-1991: Visiting Assistant Professor, Mathematics Dept., University of Southern California, Los Angeles, USA
  • 1989-1990: Postdoc, Mathematics Dept., University of Southern California, Los Angeles, USA
  • 1988-1989: Postdoc, Mathematics Dept., University of Bielefeld, Germany

Awards and Honors

  • since April 2012: Visiting Professor at Division of theoretical Genetics, National Institute of Genetics, Mishima, Japan
  • 2005: Award of the WWTF Science Chairs, Vienna, Austria
  • since 1999: Honorary Professor for Theoretical Biology, University of Leipzig, Germany
  • 1985-1988: PhD scholarship, Studienstiftung des Deutschen Volkes, Germany

Publications

    2024

  • O. Chernomor, C. Elgert, and A. von Haeseler (2024) Gentrius: generating trees compatible with a set of unrooted subtrees and its application to phylogenetic terraces. Mol. Biol. Evol., 41, msae219. (DOI: 10.1093/molbev/msae219, PMID: 39431557, PMCID: PMC11536181)
  • M. Fahrenberger, C. Esk, and A. von Haeseler (2024) GTestimate: Improving relative gene expression estimation in scRNA-seq using the Good-Turing estimator. bioRxiv, 2024.07.02.601501 (DOI: 10.1101/2024.07.02.601501)
  • L. Holcik, A. von Haeseler, and F.G. Pflug (2024) GuaCAMOLE: GC-bias aware estimation improves the accuracy of metagenomic species abundances. bioRxiv, 2024.09.20.614100 (DOI: 10.1101/2024.09.20.614100)
  • A.F. Leuchtenberger and A. von Haeseler (2024) Learning from an Artificial Neural Network in Phylogenetics. IEEE/ACM Trans. Comput. Biol. Bioinform., 21, 278-288. (DOI: 10.1109/TCBB.2024.3352268, PMID: 38198267)
  • D. Lindenhofere, S. Haendelere, C. Eske, J.B. Littleboye, C. Brunet Avalos, J. Naas, F.G. Pflug, E.G.P. van de Ven, D. Reumann, A.D. Baffet, A. von Haeseler, and J.A. Knoblich (2024) Cerebral organoids display dynamic clonal growth and tunable tissue replenishment. Nat. Cell Biol., 26, 710-718. (DOI: 10.1038/s41556-024-01412-z, PMID: 38714853)
    e contributed equally
  • J. Müller, C. Hartwig, M. Sonntag, L. Bitzer, C. Adelmann, Y. Vainshtein, K. Glanz, S.O. Decker, T. Brenner, G.F. Weber, A. von Haeseler, and K. Sohn (2024) A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma. Genome Res., 34, 1185-1195. (DOI: 10.1101/gr.279326.124, PMID: 39271293)
  • J. Naase, M. Balmanae, L. Holcik, M. Novatchkova, L. Dobnikar, T. Krausgruber, S. Ladstatter, C. Bock, A. von Haeseler, C. Esk, and J.A. Knoblich (2024) Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols. bioRxiv, 2024.11.15.623576 (DOI: 10.1101/2024.11.15.623576)
    e contributed equally
  • F.G. Pflug, S. Haendeler, C. Esk, D. Lindenhofer, J.A. Knoblich, and A. von Haeseler (2024) Neutral competition explains the clonal composition of neural organoids. PLoS Comput. Biol., 20, e1012054. (DOI: 10.1371/journal.pcbi.1012054, PMID: 38648250)
  • N. Popitsch, T. Neumann, A. von Haeseler, and S.L. Ameres (2024) Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework. Genome Biol., 25, 166. (DOI: 10.1186/s13059-024-03313-8, PMID: 38918865)

    • 2023

  • S. Burgstaller-Muehlbacher, S.M. Crotty, H.A. Schmidt, F. Reden, T. Drucks, and A. von Haeseler (2023) ModelRevelator: Fast phylogenetic model estimation via deep learning. Mol. Phylogenet. Evol., 188, 107905. (DOI: 10.1016/j.ympev.2023.107905, PMID: 37595933)
  • O. Chernomor, C. Elgert, and A. von Haeseler (2023) Gentrius: generating trees compatible with a set of unrooted subtrees and its application to phylogenetic terraces. bioRxiv, 2023.01.19.524678 (DOI: 10.1101/2023.01.19.524678)
  • E.I. Kiselev, F. Pflug, and A. von Haeseler (2023) Critical growth of cerebral tissue in organoidsI: theory and experiments. Phys. Rev. Lett., 131, 178402. (DOI: 10.1103/PhysRevLett.131.178402, PMID: 37955473)
  • L.F. Paulin, M. Raveendran, R.A. Harris, J. Rogers, A. von Haeseler und F.J. Sedlazeck (2023) SVhound: Detection of regions that harbor yet undetected Structural Variation. BMC Bioinform., 24, 23. (DOI: 10.1186/s12859-022-05046-6, PMID: 36670361, software)

    • 2022

  • A. Gosselink, T. Hofer, E. Criado-Moronati, A. von Haeseler and J. Kollet (2022) InspectorCell: Finding Ground Truth in Multiplexed Microscopy Images. J. Open Source Softw., 7, 4949. (DOI: 10.21105/joss.04949)
  • M. Huth, L. Santini, E. Galimberti, J. Ramesmayer, F. Titz-Teixeira, R. Sehlke, M. Oberhuemer, S. Stummer, V. Herzog, M. Garmhausen, M. Romeike, A. Chugunova, K.F. Leesch, L. Holcik, K. Weipoltshammer, A. Lackner, C. Schoefer, A. von Haeseler, C. Buecker, A. Pauli, S. Ameres, A. Smith, A. Beyer, and M. Leeb (2022) NMD is required for timely cell fate transitions by fine-tuning gene expression and regulating translation. Genes Dev., 36, 348-367. (DOI: 10.1101/gad.347690.120, PMID: 35241478)
  • J. Kaczanowskae, F. Ganglbergere, O. Chernomore, D. Kargl, B. Galik, A. Hess, Y. Moodley, A. von Haeseler, K. Bühler, and W. Haubensak (2022) Molecular archaeology of human cognitive traits. Cell Rep., 40, 111287. (DOI: 10.1016/j.celrep.2022.111287, PMID: 36044840)
    e contributed equally
  • Á. Vértesy, O.L. Eichmueller, J. Naas, M. Novatchkova, C. Esk, M. Balmaña, S. Ladstaetter, C. Bock, A. von Haeseler, and J.A. Knoblich (2022) Gruffi: an algorithm for computational removal of stressed cells from brain organoid transcriptomic datasets. EMBO J., 41, e111118. (DOI: 10.15252/embj.2022111118, PMID: 35919947, software)

    • 2021

  • O. Chernomore, L. Peterse, J. Schneidewinde, A. Loeschcke, E. Knieps-Grünhagen, F. Schmitz, E. von Lieres, R.J. Kutta, V. Svensson, K.-E. Jaeger, T. Drepper, A. von Haeseler, and U. Krauss (2021) Complex evolution of light-dependent protochlorophyllide oxidoreductases in aerobic anoxygenic phototrophs: origin, phylogeny and function. Mol. Biol. Evol., 38, 819-837. (DOI: 10.1093/molbev/msaa234, PMID: 32931580)
    e contributed equally
  • I. Ferreira, S. Lepuschitz, S. Beisken, G. Fiume, K. Mrazek, B.J.H. Frank, S. Huber, M.A. Knoll, A. von Haeseler, A. Materna, J.G. Hofstaetter, A.E. Posch, and J. Weinberger (2021) Culture-Free Detection of Antibiotic Resistance Markers from Native Patient Samples by Hybridization Capture Sequencing. Microorganisms, 9, 1672. (DOI: 10.3390/microorganisms9081672, PMID: 34442751, PMCID: PMC8398375)
  • B.M. Fontinha, T. Zekoll, M. Al-Rawi, M. Gallach, F. Reithofer, A.J. Barker, M. Hofbauer, R.M. Fischer, A. von Haeseler, H. Baier, and K. Tessmar-Raible (2021) TMT-Opsins differentially modulate medaka brain function in a context-dependent manner. PLoS Biol., 19, e3001012. (DOI: 10.1371/journal.pbio.3001012, PMID: 33411725)
  • T.S. Kaiser, A. von Haeseler, K. Tessmar-Raible, and D.G. Heckel (2021) Timing strains of the marine insect Clunio marinus evolved and persist in the face of gene flow. Mol. Ecol., 30, 1264-1280. (DOI: 10.1111/mec.15791, PMID: 33410230)
  • M.-T. Kurzbauer, M.P. Janisiw, L.F. Paulin, I. Prusén Mota, K. Tomanov, O. Krsicka, A. von Haeseler, V. Schubert, and Peter Schlögelhofer (2021) ATM controls meiotic DNA double-strand break formation and recombination and affects synaptonemal complex organization in plants. Plant Cell, 33, 1633-1656. (DOI: 10.1093/plcell/koab045, PMID: 33659989)
  • L. Lüftinger, I. Ferreira, B.J.H. Frank, S. Beisken, J. Weinberger, A. von Haeseler, T. Rattei, J.G. Hofstaetter, A.E. Posch, and A. Materna (2021) Predictive Antibiotic Susceptibility Testing by Next-Generation Sequencing for Periprosthetic Joint Infections: Potential & Limitations. Biomedicines, 9, 910. (DOI: 10.3390/biomedicines9080910, PMID: 34440114, PMCID: PMC8389688)
  • J. Sims, F.A. Rabanal, C. Elgert, A. von Haeseler, and P. Schlögelhofer (2021) It's just a matter of time: Balancing Homologous Recombination and Non-Homologous End Joining at the rDNA Locus during Meiosis. Front. Plant Sci., 12, 773052. (DOI: 10.3389/fpls.2021.773052, PMID: 33452254, PMCID: PMC8580885)
  • J. Sims, G. Sestini, C. Elgert, A. von Haeseler, and P. Schlögelhofer (2021) Sequencing of the Arabidopsis NOR2 reveals its distinct organization and tissue-specific rRNA ribosomal variants. Nat. Commun., 12, 1-13. (DOI: 10.1038/s41467-020-20728-6, PMID: 33452254, PMCID: PMC7810690)

    • 2020

  • S.M. Crotty, B.Q. Minh, N.G. Bean, B.R. Holland, J. Tuke, L.S. Jermiin, and A. von Haeseler (2020) GHOST: Recovering Historical Signal from Heterotachously-evolved Sequence Alignments . Syst. Biol., 69, 249-264. (DOI: 10.1093/sysbio/syz051, PMID: 31364711, software)
  • C. Esk, D. Lindenhofer, S. Haendeler, R.A. Wester, F.G. Pflug, B. Schroeder, J.A. Bagley, U. Elling, J. Zuber, A. von Haeseler, and J.A. Knoblich (2020) A human tissue screen identifies a regulator of ER secretion as a brain size determinant. Science, 370, 935-941. (DOI: 10.1126/science.abb5390, PMID: 33122427)
  • I. Ferreira, S. Beisken, L. Lueftinger, T. Weinmaier, M. Klein, J. Bacher, R. Patel, A. von Haeseler, and A.E. Posch (2020) Species Identification and Antibiotic Resistance Prediction by Analysis of Whole Genome Sequence Data Using ARESdb: An Analysis of Isolates from the Unyvero Lower Respiratory Tract Infection Trial. J. Clin. Microbiol., 58, e00273-20. (DOI: 10.1128/JCM.00273-20, PMID: 32295890)
  • E. Janisiw, M. Raices, F. Balmir, L.F. Paulin, A. Baudrimont, A. von Haeseler, J. Yanowitz, V. Jantsch, and N. Silva (2020) Poly(ADP-ribose) glycohydrolase coordinates meiotic DNA double-strand break induction and repair independent of its catalytic activity. Nat. Commun., 11, 4869. (DOI: 10.1038/s41467-020-18693-1, PMID: 32978394)
  • A.F. Leuchtenbergere, S.M. Crottye, T. Drucks, H.A. Schmidt, S. Burgstaller-Muehlbacher, and A. von Haeseler (2020) Distinguishing Felsenstein Zone From Farris Zone Using Neural Networks. Mol. Biol. Evol., 37, 3632-3641. (free reprint, DOI: 10.1093/molbev/msaa164, PMID: 32637998, software)
    e contributed equally
  • N. Mahfouz, I. Ferreira, S. Beisken, A. von Haeseler, A. Posch (2020) Large-Scale Assessment of Antimicrobial Resistance Marker Databases for Genetic Phenotype Prediction. J. Antimicrob. Chemother., 75, 3099–3108. (DOI: 10.1093/jac/dkaa257, PMID: 32658975)
  • C. Manuel and A. von Haeseler (2020) Structure of the space of taboo-free sequences. J. Math. Biol., 81, 1029-1057. (DOI: 10.1007/s00285-020-01535-5, PMID: 32940748, PMCID: PMC7560954)
  • B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeselers, and R. Lanfears (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., 37, 1530-1534. (free reprint, DOI: 10.1093/molbev/msaa015, PMID: 32011700, software)
    s co-senior authors.
  • N. Popitsch, C.D. Huber, I. Buchumenski, E. Eisenberg, M. Jantsch, A. von Haeseler and M. Gallach (2020) A-to-I RNA editing uncovers hidden signals of adaptive genome evolution in animals. Genome Biol. Evol., 12, 345-357. (DOI: 10.1093/gbe/evaa046, PMID: 32145015)
  • C. Prakash, F.C. Trognitz, P. Venhuizen, A. von Haeseler, and Bodo Trognitz (2020) A Compendium of Genome-Wide Sequence Reads From NBS (Nucleotide Binding Site) Domains of Resistance Genes in the Common Potato. Sci. Rep., 10, 11392. (DOI: 10.1038/s41598-020-67848-z, PMID: 32647195)

    • 2019

  • A. Jain, D. Perisa, F. Fliedner, A. von Haeseler, and I. Ebersberger (2019) The evolutionary traceability of a protein. Genome Biol. Evol., 11, 531–545. (DOI: 10.1093/gbe/evz008, PMID: 30649284)
  • M. Krunic, P. Venhuizen, L. Müllauer, B. Kaserer and A. von Haeseler (2019) VARIFI – Web-based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data. J. Pers. Med., 9, 10. (DOI: 10.3390/jpm9010010, PMID: 30717290
  • T. Neumann, V.A. Herzog, M. Muhar, A. von Haeseler, J. Zuber; S.L. Ameres, and P. Rescheneder (2019) Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets. BMC Bioinform., 20, 258. (DOI: 10.1186/s12859-019-2849-7, PMID: 31109287)
  • S. Schenk, S. Bannister, F.J. Sedlazeck, D. Anrather, B.Q. Minh, A. Bileck, M. Hartl, A. von Haeseler, C. Gerner, F. Raible, and K. Tessmar-Raible (2019) Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase. eLife, 8, e41556. (DOI: 10.7554/eLife.41556.001, PMID: 30767890)
  • D. Schrempf, B.Q. Minh, A. von Haeseler, and C. Kosiol (2019) Polymorphism-aware species trees with advanced mutation models, bootstrap and rate heterogeneity. Mol. Biol. Evol., 35, 1294–1301. (free reprint, DOI: 10.1093/molbev/msz043, PMID: 30825307)
  • S. Uhse, F.G. Pflug, A. von Haeseler, and A. Djamei (2019) Insertion pool sequencing for insertional mutant analysis in complex host-microbe interactions. Current Protocols in Plant Biology, 4, e20086. (DOI: 10.1002/cppb.20097, PMID: 31479207)

    • 2018

  • R. Alves, B.Q. Minh, T. Urich, A. von Haeseler, and C. Schleper (2018) Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes. Nat. Commun., 9, 1517. (DOI: 10.1038/s41467-018-03861-1, PMID: 29666365, PMCID: PMC5904100)
  • D.T. Hoange, O. Chernomore, A. von Haeseler, B.Q. Minhc, and L.S. Vinhc (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35, 518-522. (free reprint, DOI: 10.1093/molbev/msx281, PMID: 29077904, software)
    e contributed equally, c corresponding authors.
  • D.T. Hoang, L.S. Vinh, T. Flouri, A. Stamatakis, A. von Haeselerc, and B.Q. Minhc (2018) MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC Evol. Biol., 18, 11. (DOI: 10.1186/s12862-018-1131-3, PMID: 29390973, software)
    c corresponding authors.
  • M. Muhar, A. Ebert, T. Neumann, C. Umkehrer, J. Jude, C. Wieshofer, P. Rescheneder, J.J. Lipp, V.A. Herzog, B. Reichholf, D.A. Cisneros, T. Hoffmann, M.F. Schlapansky, P. Bhat, A. von Haeseler, T. Köcher, A.C. Obenauf, J. Popow, S.L. Ameres, and J. Zuber (2018) SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis. Science, 360, 800-805. (DOI: 10.1126/science.aao2793, PMID: 29622725)
  • C. Müller, M. Krunic, J. Wendt, A. von Haeseler, and I. Okamoto (2018) Germline variants in the POT1-gene in high-risk melanoma patients in Austria. G3-Genes Genomes Genet., 8, 1475-1480. (DOI: 10.1534/g3.117.300394, PMID: 29523635)
  • L.-T. Nguyen, A. von Haeseler, and B.Q. Minh (2018) Complex models of sequence evolution require accurate estimators as exemplified with the invariable site plus Gamma model. Syst. Biol., 67, 552-558. (DOI: 10.1093/sysbio/syx092, PMID: 29186593, software)
  • F.G. Pflug and A. von Haeseler (2018) TRUmiCount: Correctly counting absolute numbers of molecules using unique molecular identifiers. Bioinformatics, 34, 3137-3144. (DOI: 10.1093/bioinformatics/bty283, PMID: 29672674, software)
  • F.J. Sedlazecke, P. Reschenedere, M. Smolka, H. Fang, M. Nattestad, A. von Haeseler, and M.C. Schatz (2018) Accurate detection of complex structural variations using single molecule sequencing. Nat. Meth., 15, 461-468. (DOI: 10.1038/s41592-018-0001-7, PMID: 29713083)
    e contributed equally
  • S. Uhse, F.G. Pflug, A. Stirnberg, K. Ehrlinger, A. von Haeseler, and A. Djamei (2018) In vivo Insertion Pool Sequencing identifies Virulence Factors in a complex Fungal-Host Interaction. PLoS Biol., 16, e2005129. (DOI: 10.1371/journal.pbio.2005129, PMID: 29684023)

    • 2017

  • V.A. Herzog, B. Reichholf, T. Neumann, P. Rescheneder, P. Bhat, T.R. Burkard, W. Wlotzka, A. von Haeseler, J. Zuber, and S.L. Ameres (2017) Thiol-linked alkylation for the metabolic sequencing of RNA. Nat. Methods, 14, 1198-1204. (DOI: 10.1038/nMeth.4435, PMID: 28945705)
  • S. Kalyaanamoorthye, B.Q. Minhe, T.K.F. Wonge, A. von Haeseler, and L.S. Jermiin (2017) ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates. Nat. Methods, 14, 587-589. (DOI: 10.1038/nmeth.4285, PMID: 28481363) PMCID: PMC5453245) software) press release by MFPL
    e contributed equally
  • C. Prakash and A. von Haeseler (2017) An Enumerative Combinatorics Model for Fragmentation Patterns in RNA Sequencing Provides Insights into Non-uniformity of the Expected Fragment Starting Point and Coverage Profile. J. Comput. Biol., 24, 200-212. (DOI: 10.1089/cmb.2016.0096, PMID: 27661099)
  • O. Ratmann, C. Wymant, C. Colijn, S. Danaviah, M. Essex, S.D.W. Frost, A. Gall, S. Gaiseitsiwe, M. Grabowski, R. Gray, S. Guindon, A. von Haeseler, P. Kaleebu, M. Kendall, A. Kozlov, J. Manasa, B.Q. Minh, S. Moyo, V. Novitsky, R. Nsubuga, S. Pillay, T.C. Quinn, D. Serwadda, D. Ssemwanga, A. Stamatakis, J. Trifinopoulos, M. Wawer, A. Leigh Brown, T. de Oliveira, P. Kellam, D. Pillay, and C. Fraser (2017) HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences. AIDS Res. Hum. Retrovir., 33, 1083-1098. (DOI: 10.1089/AID.2017.0061, PMID: 28540766)

    • 2016

  • O. Chernomor, A. von Haeseler, and B.Q. Minh (2016) Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices. Syst. Biol., 65, 997-1008. (free reprint, DOI: 10.1093/sysbio/syw037, PMID: 27121966, software)
  • O. Chernomor, S. Klaere, A. von Haeseler, and B.Q. Minh (2016) Split diversity: measuring and optimizing biodiversity using phylogenetic split networks. In R. Pellens and P. Grandcolas (eds.) Biodiversity Conservation and Phylogenetic Systematics (Series: Topics in Biodiversity and Conservation, Vol. 14), 173-195, Springer, Heidelberg/New York. (DOI: 10.1007/978-3-319-22461-9_9, book-DOI: 10.1007/978-3-319-22461-9_9, eISBN: 978-3-319-22461-9, ISBN: 978-3-319-22460-2)
  • K. Gessone, P. Reschenedere, M.P. Skoruppa, A. von Haeseler, T. Dechat, and R. Foisner (2016) A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha. Genome Res., 26, 462-473. (DOI: 10.1101/gr.196220.115, PMID: 26798136)
    e contributed equally
  • S. Grumaze, P. Stevense, C. Grumaz, S. Decker, M. Weigand, S. Hofer, T. Brenner, A. von Haeseler, and K. Sohn (2016) Next-generation sequencing diagnostics of bacteremia in septic patients. Genome Med., 8:73. (DOI: 10.1186/s13073-016-0326-8, PMID: 27368373)
    e contributed equally
  • D.T. Hoang, L.S. Vinh, T. Flouri, A. Stamatakis, A. von Haeseler, and B.Q. Minh (2016) A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation. Proceedings of the 8th International Conference on Knowledge and Systems Engeneering - KSE-2016 (Hanoi, Vietnam), 1-6, IEEE Computer Society, Piscataway, NJ, USA. (DOI: 10.1109/KSE.2016.7758020)
  • M. Jagut, P. Hamminger, A. Woglar, S. Millonigg, L.F. Paulin, M. Mikl, M.R. Dello Stritto, L. Tang, C. Habacher, A. Tam, M. Gallach, A. von Haeseler, A.M. Villeneuve, V. Jantsch (2016) Separable Roles for a Caenorhabditis elegans RMI1 Homolog in Promoting and Antagonizing Meiotic Crossovers Ensure Faithful Chromosome Inheritance. PLoS Biol., 14, e1002412. (DOI: 10.1371/journal.pbio.1002412) PMID: 27011106, PMCID: PMC4807110)
  • T.S. Kaiser, B. Poehn, D. Szkiba, M. Preussner, F.J. Sedlazeck, A. Zrim, T. Neumann, L.-T. Nguyen, A.J. Betancourt, T. Hummel, H. Vogel, S. Dorner, F. Heyd, A. von Haeseler, and K. Tessmar-Raible (2016) The genomic basis of circadian and circalunar timing adaptations in a midge. Nature, 540, 69-73. (DOI: 10.1038/nature20151, PMID: 27871090, PMCID: PMC5133387, ClunioBase)
  • D. Schrempf, B.Q. Minh, N. De Maio, A. von Haeseler, and C. Kosiol (2016) Reversible polymorphism-aware phylogenetic models and their application to tree inference. J. Theor. Biol., 407, 362-370. (DOI: 10.1016/j.jtbi.2016.07.042, PMID: 27480613, software) # bioRxiv-preprint-DOI:10.1101/048496)
  • J. Trifinopoulos, L.-T. Nguyen, A. von Haeseler, and B.Q. Minh (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res., 44, W232-W235. (free reprint, DOI: 10.1093/nar/gkw256, PMID: 27084950, W-IQ-TREE webserver)

    • 2015

  • O. Chernomor, B.Q. Minhc, F. Forest, S. Klaere, T. Ingram, M. Henzinger, and A. von Haeseler (2015) Split Diversity in Constrained Conservation Prioritization using Integer Linear Programming. Methods Ecol. Evol., 6, 83-91. (DOI: 10.1111/2041-210X.12299), c corresponding author
  • O. Chernomor, B.Q. Minh, and A. von Haeseler (2015) Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference. J. Comput. Biol., 22, 1129-1142. (DOI: 10.1089/cmb.2015.0146, PMID: 26448206)
  • C. Fieber, N. Gratz, T. Koestler, X.-D. Li, V. Castiglia, M. Janos, M. Aberle, M. Sauert, M. Wegner, L. Alexopoulou, C.J. Kirschning, Z.J. Chen, A. von Haeseler, and P. Kovarik (2015) Innate immune response to Streptococcus pyogenes depends on the combined activation of TLR13 and TLR2. PLoS ONE, 10, e0119727. (DOI: 10.1371/journal.pone.0119727, PMID: 25756897)
  • T. Flouri, F. Izquierdo-Carrasco, D. Darriba, A.J. Aberer, L.-T. Nguyen, B.Q. Minh, A. von Haeseler, and A. Stamatakis (2015) The phylogenetic Likelihood Library. Syst. Biol., 64, 356-362. (DOI: 10.1093/sysbio/syu084, PMID: 25358969, software)
  • M. Krunice, R. Ertle, B. Hagen, F.J. Sedlazeck, R. Hofmann-Lehmann, A. von Haeseler and D. Klein (2015) Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study. BMC Vet. Res., 11, 90. (DOI: 10.1186/s12917-015-0378-9, PMID: 25879730)
    e contributed equally
  • L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, and B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol., 32, 268-274. (free reprint, DOI: 10.1093/molbev/msu300, PMID: 25371430, PMCID: PMC4271533, software)
  • M. Smolka, P. Rescheneder, M. Schatz, A. von Haeseler, and F.J. Sedlazeck (2015) Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol., 16, 235. (DOI: 10.1186/s13059-015-0803-1, PMID: 26494581, PMCID: PMC4618857, Teaser webpage)
  • M. Tscherner, F. Zwolanek, S. Jenull, F.J. Sedlazeck, A. Petryshyn, I.E. Frohner, J. Mavrianos, N. Chauhan, A. von Haeseler, and K. Kuchler (2015) The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways. PLoS Pathog., 11, e1005218. (DOI: 10.1371/journal.ppat.1005218, PMID: 26473952)

    • 2014

  • A.D. Chipman, D.E.K. Ferrier, C. Brena, J. Qu, D.S.T. Hughes, R. Schröder, M. Torres-Oliva, N. Znassi, H. Jiang, F.C. Almeida, C.R. Alonso, Z. Apostolou, P. Aqrawi, W. Arthur, J.C.J. Barna, K.P. Blankenburg, D. Brites, S. Capella-Gutierrez, M. Coyle, P.K. Dearden, L. Du Pasquier, E.J. Duncan, D. Ebert, C. Eibner, G. Erikson, P.D. Evans, C.G. Extavour, L. Francisco, T. Gabaldon, W.J. Gillis, E.A. Goodwin-Horn, J.E. Green, S. Griffiths-Jones, C.J.P. Grimmelikhuijzen, S. Gubbala, R. Guido, Y. Han, F. Hauser, P. Havlak, L. Hayden, S. Helbing, M. Holder, J.H.L. Hui, J.P. Hunn, V.S. Hunnekuhl, L. Jackson, M. Javaid, S.N. Jhangiani, F.M. Jiggins, T.E. Jones, T.S. Kaiser, D. Kalra, N.J. Kenny, V. Korchina, C.L. Kovar, F.B. Kraus, F. Lapraz, S.L. Lee, J. Lv, C. Mandapat, G. Manning, M. Mariotti, R. Mata, T. Mathew, T. Neumann, I. Newsham, D.N. Ngo, M. Ninova, G. Okwuonu, F. Ongeri, W.J. Palmer, S. Patil, P. Patraquim, C. Pham, L.-L. Pu, N.H. Putman, C. Rabouille, O. Mendivil Ramos, A.C. Rhodes, H.E. Robertson, H.M. Robertson, M. Ronshaugen, J. Rozas, N. Saada, A. Sanchez-Gracia, S.E. Scherer, A.M. Schurko, K.W. Siggens, D. Simmons, A. Stief, E. Stolle, M.J. Telford, K. Tessmar-Raible, R. Thornton, M. van der Zee, A. von Haeseler, J.M. Williams, J.H. Willis, Y. Wu, X. Zou, D. Lawson, D.M. Muzny, K.C. Worley, R.A. Gibbs, M. Akam, and S. Richards (2014) The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima. PLoS Biol., 12, e1002005. (DOI: 10.1371/journal.pbio.1002005, PMID: 25423365, PMCID: PMC4244043)
  • E. Dell'Ampioe, K. Meusemanne, N.U. Szucsiche, R.S. Peterse, B. Meyer, J. Borner, M. Petersen, A.J. Aberer, A. Stamatakis, M.G. Walzl, B.Q. Minh, A. von Haeseler, I. Ebersberger, G. Pass, and B. Misof (2014) Decisive Datasets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects. Mol. Biol. Evol., 31, 239-249. (DOI: 10.1093/molbev/mst196, PMID: 24140757)
    e contributed equally
  • I. Ebersberger and A. von Haeseler (2014) Exploring phylogenomic data. In J.W. Waegele, T. Bartholomaeus (eds.) Deep Metazoan Phylogeny: The Backbone of the Tree of Life., 595-617, De Gruyter, Berlin. (DOI: 10.1515/9783110277524.595, eISBN: 9783110277524)
  • I. Ebersberger, S. Simm, M. Leisegang, P. Schmitzberger, O. Mirus, A. von Haeseler, M. Bohnsack, and E. Schleiff (2014) The evolution of the ribosome biogenesis pathway from a yeast perspective. Nucleic Acids Res., 42, 1509-1523. (DOI: 10.1093/nar/gkt1137, PMID: 24234440)
  • M. Kaschner, A. Loeschcke, J. Krause, B.Q. Minh, A. Heck, S. Endres, V. Svensson, A. Wirtz, A. von Haeseler K.-E. Jaeger, T. Drepper, and U. Krauss (2014) Discovery of the first light-dependent protochlorophyllide oxidoreductase in anoxygenic phototrophic bacteria. Mol. Microbiol., 93, 1066-1078. (DOI: 10.1111/mmi.12719, PMID: 25039543)
  • G. Sengoelge, W. Winnicki, A. Kupczok, A. von Haeseler, M. Schuster, W. Pfaller, P. Jennings, A. Weltermann, S. Blake, and G. Sunder-Plassmann (2014) A SAGE based approach to human glomerular endothelium: defining the transcriptome, finding a novel molecule and highlighting endothelial diversity. BMC Genomics, 15, 725. (DOI: 10.1186/1471-2164-15-725, PMID: 25163811, PMCID: PMC4156628)
  • D. Szkiba, M. Kapun, A. von Haeseler, and M. Gallach (2014) SNP2GO: functional analysis of genome-wide association studies. Genetics, 197, 285-289. (DOI: 10.1534/genetics.113.160341, PMID: 24561481, software)
  • C. Vesely, S. Tauber, F. Sedlazeck, M. Tajaddod, A. von Haeseler, and M. Jantsch (2014) ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain. Nucleic Acids Res., 42, 2155-12168. (DOI: 10.1093/nar/gku844, PMID: 25260591)

    • 2013

  • M. Anisimova, D.A. Liberles, H. Philippe, J. Provan, T. Pupko, and A. von Haeseler (2013) State-of the art methodologies dictate new standards for phylogenetic analysis. BMC Evol. Biol., 13, 161. (DOI: 10.1186/1471-2148-13-161, PMID: 23914788, PMCID: PMC3751533)
  • S. Jünemann, F.J. Sedlazeck, K. Prior, A. Albersmeier, U. John, J. Kalinowski, A. Mellmann, A. Goesmann, A. von Haeseler, J. Stoye and D. Harmsen (2013) Updating benchtop sequencing performance comparison. Nat. Biotechnol., 31, 294-296. (DOI: 10.1038/nbt.2522, PMID: 23563421)
  • B.Q. Minh, M.A.T. Nguyen, and A. von Haeseler (2013) Ultra-Fast Approximation for Phylogenetic Bootstrap. Mol. Biol. Evol., 30, 1188-1195. (free reprint, DOI: 10.1093/molbev/mst024, PMID: 23418397, software)
  • N. Popitsch and A. von Haeseler (2013) NGC: Lossless and Lossy Compression of Aligned High-throughput Sequencing Data. Nucleic Acids Res., 41, e27. (free reprint, DOI: 10.1093/nar/gks939, PMID: 23066097, software)
  • F.J. Sedlazecke, P. Reschenedere, and A. von Haeseler (2013) NextGenMap: Fast and accurate read mapping in highly polymorphic genomes. Bioinformatics, 29, 2790-2791. (DOI: 10.1093/bioinformatics/btt468, PMID: 23975764, software)
    e contributed equally
  • F.J. Sedlazeck, P. Talloji, A. von Haeseler, and A. Bachmair (2013) Benefit-of-doubt (BOD) scoring: a sequencing-based method for SNP candidate assessment from high to medium read number data sets. Genomics, 101, 204-209. (DOI: 10.1016/j.ygeno.2012.12.001, PMID: 23246509)
  • S. Tauber and A. von Haeseler (2013) Exploring the sampling universe of RNA-seq. Stat. Appl. Genet. Mol. Biol. (SAGMB), 12, 175-188. (DOI: 10.1515/sagmb-2012-0049, PMID: 23629158)

    • 2012

  • H.Q. Dinh, M. Dubine, F.J. Sedlazecke, N. Lettner, O. Mittelsten Scheid, and A. von Haeseler (2012) Advanced Methylome Analysis after Bisulfite Deep Sequencing: an Example in Arabidopsis. PLoS ONE, 7, e41528. (DOI: 10.1371/journal.pone.0041528, PMID: 22911809, PMCID: PMC3401099)
    e contributed equally
  • I. Ebersberger, R. de Matos Simoes, A. Kupczok, M. Gube, E. Kothe, K. Voigt, and A. von Haeseler (2012) A Consistent Backbone for the Fungi. Mol. Biol. Evol., 29, 1319-1334. (DOI: 10.1093/molbev/msr285, PMID: 22114356)
  • M. Fischer, S. Klaere, M.A.T. Nguyen and A. von Haeseler (2012) On the group theoretical background of assigning stepwise mutations onto phylogenies. Algoritms Mol. Biol., 7, 36. (DOI: 10.1186/1748-7188-7-36, PMID: 23241267)
  • A. von Haeseler (2012) Do we still need supertrees? BMC Biol., 10, 13. (DOI: 10.1186/1741-7007-10-13, PMID: 22369571)
  • T. Köstler, A. von Haeseler, and I. Ebersberger (2012) REvolver: Modeling sequence evolution under domain constraints. Mol. Biol. Evol., 29, 2133-2145. (DOI: 10.1093/molbev/mss078, PMID: 2383532)
  • T. Laubach, A. von Haeseler, and M.J. Lercher (2012) TreeSnatcher plus: capturing phylogenetic trees from images. BMC Bioinform., 13, 110. (DOI: 10.1186/1471-2105-13-110, PMID: 22624611)
  • M.A.T. Nguyen, T. Gesell, and A. von Haeseler (2012) ImOSM: Intermittent Evolution and Robustness of Phylogenetic Methods. Mol. Biol. Evol., 29, 663-673. (free reprint, DOI: 10.1093/molbev/msr220, PMID: 21940641)
  • S. Reitter-Pfoertner, A. von Haeseler B. Horvath, R. Sunder-Plassmann, V. Tiedje, I. Pabinger, and C. Mannhalter (2012) Identification of an ancient haemophilia A splice site mutation. Thromb. Res., 130, 445-450. (DOI: 10.1016/j.thromres.2012.02.008, PMID: 22401796)
  • P. Rescheneder, A. von Haeseler, and F.J. Sedlazeck (2012) MASon: Million Alignments In Seconds - A Platform Independent Pairwise Sequence Alignment Library for Next Generation Sequencing Data. Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2012), 195-201, SciTePress, Setubal, Portugal. (DOI: 10.5220/0003775701950201)
  • C. Veselye, S. Taubere, F.J. Sedlazeck, A. von Haeseler, and M.F. Jantsch (2012) Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs. Genome Res., 22, 1468-1476. (DOI: 10.1101/gr.133025.111, PMID: 22310477)
    e contributed equally

    • 2011

  • M.A.T. Nguyen, S. Klaere, and A. von Haeseler (2011) MISFITS: Evaluating the goodness of fit between a phylogenetic model and an alignment. Mol. Biol. Evol., 28, 143-152. (free copy, DOI: 10.1093/molbev/msq180, PMID: 20643866)
  • W. Salzburger, G. Ewing, and A. von Haeseler (2011) The performance of phylogenetic algorithms in estimating haplotype genealogies with migration. Mol. Ecol., 20, 1952-1963. (DOI: 10.1111/j.1365-294X.2011.05066.x, PMID: 21457168)
  • L.S. Vinh, A. Fuehrer, and A. von Haeseler (2011) Random Tree-Puzzle leads to the Yule-Harding Distribution. Mol. Biol. Evol., 28, 873-877. (DOI: 10.1093/molbev/msq212, PMID: 20705907)

    • 2010

  • T. Baubec, H.Q. Dinh, A. Pecinka, B. Rakic, W. Rozhon, B. Wohlrab, A. von Haeseler and O. Mittelsten Scheid (2010) Cooperation of Multiple Chromatin Modifications Can Generate Unanticipated Stability of Epigenetic States in Arabidopsis. Plant Cell, 22, 34-47. (DOI: 10.1105/tpc.109.072819, PMID: 20097869)
  • H.Q. Dinh, B.Q. Minh, H.X. Huan and A. von Haeseler (2010) ACOPHY: A simple and general ant colony optimization approach for phylogenetic tree reconstruction. LNCS, 6234 (Proceedings of the 7th Intl. Conf. on Swarm Intelligence, ANTS 2010), 360-367. (DOI: 10.1007/978-3-642-15461-4_32)
  • J. Hofmann, K. Frenzel, B.Q. Minh, A. von Haeseler, A. Edelmann, R.S. Ross, D.H. Krueger, H. Meisel (2010) Quantitative detection and typing of Hepatitis D virus in human serum by real-time PCR and melting curve analysis. Diagn. Microbiol. Infect. Dis., 67, 172-179. (DOI: 10.1016/j.diagmicrobio.2010.02.003, PMID: 20466196)
  • T. Köstler, A. von Haeseler, and I. Ebersberger (2010) FACT: Functional annotation transfer between proteins with similar feature architecture. BMC Bioinform., 11, 417. (DOI: 10.1186/1471-2105-11-417, PMID: 20696036)
  • A. Kupczok, H.A. Schmidt, and A. von Haeseler (2010) Accuracy of phylogeny reconstruction methods combining overlapping gene data sets. Algorithms Mol. Biol., 5, 37. (DOI: 10.1186/1748-7188-5-37, PMID: 21134245)
  • C. Lorenz, T. Gesell, B. Zimmermann, U. Schoeberl, I. Bilusic, L. Rajkowitsch, C. Waldsich, A. von Haeseler and R. Schroeder (2010) Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts. Nucleic Acids Res., 38, 3794-3808. (DOI: 10.1093/nar/gkq032, PMID: 20348540)
  • K. Meusemann, B.M. von Reumont, S. Simon, F. Roeding, S. Strauss, P. Kück, I. Ebersberger, M. Walzl, G. Pass, S. Breuers, V. Achter, A. von Haeseler, T. Burmester, H. Hadrys, W.W. Wägele and B. Misof (2010) A phylogenomic approach to resolve the arthropod tree of life. Mol. Biol. Evol., 27, 2451-2464. (DOI: 10.1093/molbev/msq130, PMID: 20534705)
  • B.Q. Minh, S. Klaere, and A. von Haeseler (2010) SDA*: A Simple and Unifying Solution to Recent Bioinformatic Chaallenges for Conservation Genetics. Proceedings of the 2nd International Conference on Knowledge and Systems Engeneering - KSE-2010 (Hanoi, Vietnam), 33-37, IEEE Computer Society, Los Alamitos, CA, USA. (DOI: 10.1109/KSE.2010.24, ISBN: 978-0-7695-4213-3)

    • 2009

  • S.J.F. Cronin, N.T. Nehme, S. Limmer, S. Liegeois, J.A. Pospisilik, D. Schramek, A. Leibbrandt, R. de Matos Simoes, S. Gruber, U. Puc, I. Ebersberger, T. Zoranovic, G.G. Neely, A. von Haeseler, D. Ferrandon and J.M. Penninger (2009) A genome-wide in vivo RNAi screen on innate immunity to intestinal pathogenic infections. Science, 325, 340-343. (DOI: 10.1126/science.1173164, PMID: 19520911)
  • I. Ebersberger, S. Strauss, and A. von Haeseler (2009) HaMStR: Profile Hidden Markov Model Based Search for Orthologs in ESTs. BMC Evol. Biol., 9, 157. (DOI: 10.1186/1471-2148-9-157, PMID: 19586527)
  • R. Hanada, A. Leibbrandt, T. Hanada, S. Kitaoka, T. Furuyashiki, H. Fujihara, J. Trichereau, M. Paolino, F. Qadri, R. Plehm, S. Klaere, V. Komnenovic, H. Mimata, H. Yoshimatsu, N. Takahashi, A. von Haeseler, M. Bader, S. Sebnem Kilic, Y. Ueta, C. Pifl, S. Narumiya and J.M. Penninger (2009) Central control of fever and female body temperature by RANKL/RANK. Nature, 462, 505-509. (DOI: 10.1038/nature08596, PMID: 19940926)
  • U. Krausse, B.Q. Minhe, A. Losi, W. Gaertner, T. Eggert, A. von Haeselerc, and K.E. Jaeger (2009) Distribution and phylogeny of light-oxygen-voltage-blue-light-signaling proteins in the three kingdoms of life. J. Bacteriol., 191, 7234-7242. (DOI: 10.1128/JB.00923-09, PMID: 19783626)
    e contributed equally, c corresponding author
  • A. Kupczok and A. von Haeseler (2009) Comment on: A congruency index for testing topological similarity between trees. Bioinformatics, 25, 147-149. (DOI: 10.1093/bioinformatics/btn539, PMID: 18922807)
  • B.Q. Minh, S. Klaere, and A. von Haeseler (2009) Taxon Selection under Split Diversity. Syst. Biol., 57, 586-594. (DOI: 10.1093/sysbio/syp058; PMID: 20525611)
  • B.Q. Minh, F. Pardi, S. Klaere, and A. von Haeseler (2009) Budgeted Phylogenetic Diversity on Circular Split Systems. IEEE/ACM Trans. Comput. Biol. Bioinform., 6, 22-29. (DOI: 10.1109/TCBB.2008.54, PMID: 19179696)
  • O. Mirus, T. Bionda, A. von Haeseler, and E. Schleiff (2009) Evolutionarily evolved discriminators in the TPR domain of the Toc64 family involved in protein translocation at the outer membrane of chloroplasts and mitochondria. J. Mol. Mod., 15, 971-982. (DOI: 10.1007/s00894-008-0449-y, PMID: 19198901)
  • O. Miruse, S. Strausse, K. Nicolaisen, A. von Haeseler, E. Schleiff (2009) TonB-dependent transporters and their occurrence in cyanobacteria. BMC Biol., 7, 68. (DOI: 10.1186/1741-7007-7-68, PMID: 19821963)
    e contributed equally
  • H.A. Schmidt and A. von Haeseler (2009) Phylogenetic Inference Using Maximum Likelihood Methods. In P. Lemey, M. Salemi, A.M. Vandamme (eds.)The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing., 2nd Edition, 181-209, Cambridge University Press, Cambridge. (DOI: 10.1017/CBO9780511819049.008, ISBN: paperback: 9780521730716, hardcover: 9780521877107, book webpage)
  • S. Simon, S. Strauss, A. von Haeseler, and H. Hadrys (2009) A phylogenomic approach to resolve the basal pterygote divergence. Mol. Biol. Evol., 26, 2719-2730. (DOI: 10.1093/molbev/msp191, PMID: 19713325)
  • K. Strimmer and A. von Haeseler (2009) Nucleotide Substitition Models. In P. Lemey, M. Salemi, A.M. Vandamme (eds.)The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing., 2nd Edition, 111-141, Cambridge University Press, Cambridge. (ISBN: paperback: 9780521730716, hardcover: 9780521877107, book webpage)
  • M. Tillich, L.S. Vinh, K. Schulerowitz, A. von Haeseler, U.G. Maier and C. Schmitz-Linneweber (2009) Loss of MatK RNA Editing in Seed Plant Chloroplasts. BMC Evol. Biol., 9, 201. (DOI: 10.1186/1471-2148-9-201) PMID: 19678945)

    • 2008

  • I. Bruns, Ingmar and U. Steidl, Ulrich and J.C. Fischer, A. Czibere, G. Kobbe, S. Raschke, R. Singh, R. Fenk, M. Rosskopf, S. Pechtel, A. von Haeseler, P. Wernet, D. Tenen, R. Haas, and R. Kronenwett (2008) Pegylated G-CSF mobilizes CD34+ cells with different stem and progenitor subsets and distinct functional properties in comparison with unconjugated G-CSF. Haematologica, 93, 347-355. (DOI: 10.3324/haematol.12081, PMID: 18268278)
  • G.B. Ewing, I. Ebersberger, H.A. Schmidt, and A. von Haeseler (2008) Rooted Triple Consensus and Anomalous Gene Trees. BMC Evol. Biol., 8, 118. (DOI: 10.1186/1471-2148-8-118, PMID: 18439266)
  • S. Klaere, T. Gesell, and A. von Haeseler (2008) The impact of single substitutions on multiple sequence alignments. Phil. Trans. R. Soc. Lond. B, 363, 4041-4047. (DOI: 10.1098/rstb.2008.0140, PMID: 18852110)
  • A. Kupczok, A. von Haeseler, and S. Klaere (2008) An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees. J. Comput. Biol., 15, 577-591. (DOI: 10.1089/cmb.2008.0068, PMID: 18631022)
  • D. Mainz, I. Paulsen, I. Mainz, K. Weller, J. Kohl, and A. von Haeseler (2008) Knowledge Acquisition Focused Cooperative Development of Bio-Ontologies - A Case Study with BIO2Me. In M. Elloumi, J. Küng, M. Linial, R.F. Murphy, K. Schneider, T. Cristian (eds.) Bioinformatics Research and Development., 258-272, Springer, Berlin. (ISBN 978-3-540-70598-7)
  • I. Mainz, K. Weller, I. Paulsen, D. Mainz, J. Kohl, and A. von Haeseler (2008) Ontoverse: Collaborative Ontology Engineering for the Life Sciences. Inform. Wiss. Praxis, 2, 91-99. (online access)
  • A. Rohrbeck, J. Neukirchen, M. Rosskopf, G.G. Pardillos, H. Geddert, A. Schwalen, H.E. Gabbert, A. von Haeseler, G. Pitschke, M. Schott, R. Kronenwett, R. Haas, Rainer U.-P. Rohr (2008) Gene expression profiling for molecular discrimination and characterization of laser captured primary lung cancers. J. Translat. Med., 6, 69. (DOI: 10.1186/1479-5876-6-69)
  • H. Schabauer, J. Zottl, A. von Haeseler, W.N. Gansterer, and H.A. Schmidt (2008) Phylogenetic Quality Assessment for Campus Grids. In J. Küng, K. Schneider, R. Wagner (eds.) BIRD'08 -- 2nd International Conference on Bioinformatics and Development (Articles on Poster Presentations)., Schriftenreihe Informatik, 109-114, Trauner Verlag, Linz. (ISBN 978-3-85499-422-0)
  • L.S. Vinh and A. von Haeseler (2008) Bookreview on "Computational Molecular Evolution by Ziheng Yang, 2006, Oxford University Press, Oxford". Syst. Biol., 56, 1024-1026. (DOI: 10.1080/10635150701752532, PMID: 18066933)

    • 2007

  • R. Bredemeier, T. Schlegel, F. Ertel, A. Vojita, L. Borissenko, M.T. Bohnsack, M. Groll, A. von Haeseler, and E. Schleiff (2007) Functional and phylogenetic properties of the pore forming β-barrel transporter of the Omp85 family. J. Biol. Chem., 282, 1882-1890. (DOI: 10.1074/jbc.M609598200, PMID: 17088246)
  • E. Diaz-Blanco, I. Bruns, F. Neumann, J.C. Fischer, T. Graef, M. Rosskopf, B. Brors, S. Pechtel, S. Bork, A. Koch, A. Baer, U.-P. Rohr, G. Kobbe, A. von Haeseler, N. Gattermann, and R. Kronenwett (2007) Molecular signature of CD34+ hematopoietic stem and progenitor cells of patients with CML in chronic phase. Leukemia, 21, 494-504. (DOI: 10.1038/sj.leu.2404549, PMID: 17252012)
  • I. Ebersberger, P. Galgoczy, S. Taudien, S. Taenzer, M. Platzer, and A. von Haeseler (2007) Mapping human genetic ancestry. Mol. Biol. Evol., 24, 2266-2276. (DOI: 10.1093/molbev/msm156, PMID: 17660505)
  • I. Ebersberger, A. von Haeseler, and H.A. Schmidt (2007) Phylogeny Reconstruction. In T. Lengauer (ed.) Bioinformatics: From Genomes to Therapies 83-128, Wiley-VCH, Weinheim. (DOI: 10.1002/9783527619368.ch4, ISBN 978-3-527-31278-8)
  • M.R. Eckert, T. Gesell, M. Grabner, A. Gruber, K. Gonzales, I.L. Hofacker, A. von Haeseler, and E. Charpentier (2007) A bioinformatic screen reveals novel small noncoding RNAs in Streptococcus pyogenes FEBS J., 274, 189. (DOI: 10.1111/j.0014-2956.2007.05861.x)
  • T. Laubach and A. von Haeseler (2007) TreeSnatcher: Coding trees from images. Bioinformatics, 23, 3384-3385. (DOI: 10.1093/bioinformatics/btm438, PMID: 17893085)
  • S. Linz, A. Radtke, A. von Haeseler (2007) A maximum likelihood framework to measure horizontal gene transfer. Mol. Biol. Evol., 24, 1312-1319. (DOI: 10.1093/molbev/msm052, PMID: 17374878)
  • W. Löffelhardt, A. von Haeseler, E. Schleiff (2007) The β-barrel shaped polypeptide transporter, an old concept for precursor protein transfer across membranes. Symbiosis, 44, 33-42.
  • F. Roeding, S. Hagner-Holler, H. Ruhberg, I. Ebersberger, A. von Haeseler, M. Kube, R. Reinhardt, and Burmester, T. (2007) EST sequencing of Onychophora and phylogenomic analysis of Metazoa. Mol. Phylogenet. Evol., 45, 942-951. (DOI: 10.1016/j.ympev.2007.09.002, PMID: 17933557)
  • U. Schauer, C. Lorenz, T. Gesell, C. Waldsich, A. von Haeseler, and R. Schroeder (2007) Characterization of high affinity Hfq binding sites FEBS J., 274, 86. (DOI: 10.1111/j.0014-2956.2007.05861_1.x)
  • T. Schlegel, O. Mirus, A. von Haeseler and E. Schleiff (2007) The tetratricopeptide repeats of receptors involved in protein translocation across membranes. Mol. Biol. Evol., 24, 2763-2774. (DOI: 10.1093/molbev/msm211, PMID: 17905998)
  • H.A. Schmidt and A. von Haeseler (2007) Maximum Likelihood Analysis using TREE-PUZZLE. (revised version) In A.D. Baxevanis, D.B. Davison, R.D.M. Page, G. Stormo, and L. Stein (eds.) Current Protocols in Bioinformatics, 17, Unit 6.6, pages 6.6.1-6.6.23, Wiley and Sons, New York. (DOI: 10.1002/0471250953.bi0606s17, PMID: 18428792, ISBN 0-471-25093-7, CP online)
  • H.A. Schmidt, A. von Haeseler, and J. Buschbom (2007) pIPHULA - Parallel Inference of Population Parameters Using a Likelihood Approach. Bioinformatics, 23, 2636-2637. (free reprint, DOI: 10.1093/bioinformatics/btm391, PMID: 17698495)

    • 2006

  • I. Bruns, U. Steidl, J.C. Fischer, S. Raschke, G. Kobbe, R. Fenk, M. Rosskopf, S. Pechtel, U.-P. Rohr, A. von Haeseler, P. Wernet, D. Tenen, R. Haas, and R. Kronenwett (2006) Meeting Abstract: Pegylated G-CSF Mobilizes CD34+ Cells with Different Stem and Progenitor Cell Subsets and Distinct Functional Properties in Comparison with Unconjugated G-CSF. Blood, 108, 3382. (Journal site)
  • T. Gesell and A. von Haeseler (2006) In silico sequence evolution with site-specific interactions along phylogenetic trees. Bioinformatics, 22, 716-722. (DOI: 10.1093/bioinformatics/bti812, PMID: 16332711)
  • B. Kilian, H. Özkan, J. Kohl, A. von Haeseler, O. Deusch, A. Brandolini, C. Yucel, W. Martin, and F. Salamini (2006) Haplotype structure at seven barley genes: relevance to gene pool bottlenecks, phylogeny of ear type and site of barley domestication. Mol. Genet. Genomics, 275, 230-241. (DOI: 10.1007/s00438-006-0136-6, PMID: 16758198)
  • J. Kohl, I. Paulsen, T. Laubach, A. Radtke, and A. von Haeseler (2006) HvrBase++: A phylogenetic database for primate species. Nucleic Acids Res., 34, D700-D704. (DOI: 10.1093/nar/gkj030, PMID: 16381963)
  • B.Q. Minh, S. Klaere, and A. von Haeseler (2006) Phylogenetic Diversity within Seconds. Syst. Biol., 55, 769-773. (DOI: 10.1080/10635150600981604)
  • B.Q. Minh, L.S. Vinh, H.A. Schmidt, and A. von Haeseler (2006) Large Maximum Likelihood Trees. Proceedings of the NIC Symposium 2006. 357-365, Forschungszentrum Jülich, Germany. (free reprint, ISBN 3-00-017351-X)
  • I. Paulsen and A. von Haeseler (2006) INVHOGEN: A database of homologous invertebrate genes. Nucleic Acids Res., 34, D349-D353. (DOI: 10.1093/nar/gkj100, PMID: 16381884)
  • E. Petzold, D. Merkle, M. Middendorf, A. von Haeseler, and H.A. Schmidt (2006) Phylogenetic Parameter Estimation on COWs. In A.Y. Zomaya (ed.) Parallel Computing for Bioinformatics and Computational Biology 347-368, Wiley and Sons, New York. (DOI: 10.1002/0471756504.ch15, ISBN 0-471-71848-3)

    • 2005

  • J. Buschbom and A. von Haeseler (2005) Introduction to applications of the likelihood function in molecular evolution. In R. Nielsen (ed.) Statistical Methods in Molecular Evolution 25-44, Springer, New York. (ISBN: 0-387-22333-9)
  • R. Fleißner, D. Metzler, and A. von Haeseler (2005) Simultaneous statistical multiple alignment and phylogeny reconstruction. Syst. Biol., 54, 548-561. (DOI: 10.1080/10635150590950371, PMID: 16085574)
  • J. Kohl and A. von Haeseler (2005) Bookreview on "Perl Programming for Biologists by D.C. Jamison. Wiley-Liss, Chichester, 2003". Biometrics, 61, 316. (DOI: 10.1111/j.0006-341X.2005.20050217-2_6.x)
  • A. Kusserow, K. Pang, C. Sturm, M. Hrouda, J. Lentfer, H.A. Schmidt, U. Technau, A. von Haeseler, B. Hobmayer, M.Q. Martindale, and T.W. Holstein (2005) Unexpected complexity of Wnt gene family in a sea anemone. Nature, 433, 156-160. (DOI: 10.1038/nature03158, PMID: 15650739) , press releases by FZ Jülich (follow-ups: Bionity, Google search), Heidelberg University
  • D. Metzler, R. Fleißner, A. Wakolbinger, and A. von Haeseler (2005) Stochastic insertion-deletion processes and statistical sequence alignment. In A. Greven and D. Deuschel (eds.) Interacting Stochastic Systems, 247-267, Springer, Heidelberg/Berlin. (ISBN: 3-540-23033-5)
  • B.Q. Minh, L.S. Vinh, A. von Haeseler, and H.A. Schmidt (2005) pIQPNNI -- Parallel Reconstruction of Large Maximum Likelihood Phylogenies. Bioinformatics, 21:3794-3796. (free reprint, DOI: 10.1093/bioinformatics/bti594, PMID: 16046495)
  • S. Moslavac, O. Mirus, R. Bredemeier, J. Soll, A. von Haeseler, and E. Schleiff (2005) Conserved pore-forming regions in polypeptide-transporting proteins. FEBS J., 272, 1367-1378. (DOI: 10.1111/j.1742-4658.2005.04569.x, PMID: 15752354)
  • H. Oota, B. Pakendorf, G. Weiss, A. von Haeseler, S. Pookajorn, W. Settheetham-Ishida, D. Tiwawech, T. Ishida, and M. Stoneking (2005) Recent Origin and Cultural Reversion of a Hunter-Gatherer Group. PLoS Biol., 3, e71. (DOI: 10.1371/journal.pbio.0030071, PMID: 15736978)
  • L.S. Vinh, H.A. Schmidt, and A. von Haeseler (2005) PhyNav: A novel approach to reconstruct large phylogenies. In C. Weihs and W. Gaul (eds.) Classification, the Ubiquitous Challenge Series Studies in Classification, Data Analysis, and Knowledge Organization, 386-393, Springer, Heidelberg/New York. (DOI: 10.1007/3-540-28084-7_44)
  • L.S. Vinh and A. von Haeseler (2005) Shortest triplet clustering: reconstructing large phylogenies using representative sets. BMC Bioinform., 6, 92. (DOI: 10.1186/1471-2105-6-92, PMID: 15819989)

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